1F6M

CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THIOREDOXIN REDUCTASE, THIOREDOXIN, AND THE NADP+ ANALOG, AADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Twists in catalysis: alternating conformations of Escherichia coli thioredoxin reductase.

Lennon, B.W.Williams Jr., C.H.Ludwig, M.L.

(2000) Science 289: 1190-1194


  • PubMed Abstract: 
  • In thioredoxin reductase (TrxR) from Escherichia coli, cycles of reduction and reoxidation of the flavin adenine dinucleotide (FAD) cofactor depend on rate-limiting rearrangements of the FAD and NADPH (reduced form of nicotinamide adenine dinucleotid ...

    In thioredoxin reductase (TrxR) from Escherichia coli, cycles of reduction and reoxidation of the flavin adenine dinucleotide (FAD) cofactor depend on rate-limiting rearrangements of the FAD and NADPH (reduced form of nicotinamide adenine dinucleotide phosphate) domains. We describe the structure of the flavin-reducing conformation of E. coli TrxR at a resolution of 3.0 angstroms. The orientation of the two domains permits reduction of FAD by NADPH and oxidation of the enzyme dithiol by the protein substrate, thioredoxin. The alternate conformation, described by Kuriyan and co-workers, permits internal transfer of reducing equivalents from reduced FAD to the active-site disulfide. Comparison of these structures demonstrates that switching between the two conformations involves a "ball-and-socket" motion in which the pyridine nucleotide-binding domain rotates by 67 degrees.


    Related Citations: 
    • Crystal structure of Escherichia coli thioredoxin reductase refined at 2 A resolution. Implications for a large conformational change during catalysis.
      Waksman, G.,Krishna, T.S.,Sweet, R.M.,Williams Jr., C.H.,Kuriyan, J.
      (1994) J.Mol.Biol. 236: 800
    • Convergent evolution of similar function in two structurally divergent enzymes
      Kuriyan, J.,Krishna, T.S.,Wong, L.,Guenther, B.,Pahler, A.,Williams Jr., C.H.,Model, P.
      (1991) Nature 352: 172


    Organizational Affiliation

    Biophysics Research Division, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THIOREDOXIN REDUCTASE
A, B, E, F
320Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: trxB
EC: 1.8.1.9
Find proteins for P0A9P4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9P4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
THIOREDOXIN 1
C, D, G, H
108Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: trxA (fipA, tsnC)
Find proteins for P0AA25 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA25
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, E, F
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
3AA
Query on 3AA

Download SDF File 
Download CCD File 
A, B, E, F
3-AMINOPYRIDINE-ADENINE DINUCLEOTIDE PHOSPHATE
ADENOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) 2'-(DIHYDROGEN PHOSPHATE)ESTER WITH 3-(AMINO)-1-BETA-D-RIBOFURANOSYLPYRIDINIUM INNER SALT
C20 H29 N7 O16 P3
JRGQEVHOKKZPIX-HISDBWNOSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 298.929α = 90.00
b = 94.828β = 104.17
c = 79.613γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Database references